Setting up a production molecular dynamics (MD) simulation isn’t just about parameters and resources — it often begins with a critical, deceptively simple question: Which input file do I use? If you’ve ever felt unsure about which structure to load — whether it’s the right .gro file or a project from a previous stage — this post is for you.
When using the GROMACS Wizard in SAMSON, getting your input file right for a production MD run is crucial — and thankfully, it’s also made extremely efficient, if you know where to look.
Why Input Confusion Happens
Molecular modelers often work step by step: first minimization, then equilibration, and finally production MD. Each step generates output files, and knowing which one to reuse — especially under time pressure — is a known stumbling block.
For instance, if you’ve finished NPT equilibration and want to start production MD, should you load the *.gro file directly? Or the entire batch project folder? Both might work — but picking the wrong one or navigating your file system manually can easily derail the momentum of your workflow.
The ‘Auto-fill’ Option You Might Be Missing
In the Production MD step of the GROMACS Wizard, simply head over to the Simulate tab to set up your run. Here’s the trick: you can click the Auto-fill button 
, and GROMACS Wizard will intelligently populate the input path based on your last successful run.
This works whether you’re coming from an NPT equilibration step or a prior production MD run. GROMACS Wizard keeps track of your project context behind the scenes — saving you from manual file selection and minimizing the risk of mismatched input states.
Other Input Options
If you prefer, you can choose the input manually using the … button. This opens up a file selection dialog for you to point to:
- a
.grofile from an equilibration step, or - a batch project folder with prior MD runs
However, manually hunting for the correct folder or file can interrupt your modeling flow — especially after long days of working through large systems. That’s why the ‘Auto-fill’ button is worth remembering, particularly for frequent users who rely on efficient iteration cycles.
Small Feature, Big Shell Time Saver
Advanced users might enjoy the control of browsing files, but for most workflows — especially quick prototyping or educational demonstrations — automating this selection streamlines the process significantly.
Whether you’re working with a system of 19,000 atoms or more, correctly preparing the input ensures the rest of the simulation proceeds without interruptions due to inappropriate restraints or non-equilibrated states. With one click, the ‘Auto-fill’ helps guarantee continuity across simulation phases.
Missed It? Try It Next Time
If you’ve been navigating subfolders repeatedly or hesitating at the input selection dropdown, give the Auto-fill button a try during your next session. It’s small, but practical quality-of-life improvements like this one can go a long way in smoothing out the simulation setup process.
To explore the full workflow and learn more about correctly launching Production MD simulations in GROMACS Wizard, check the full documentation here:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/production-md/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.